Anna Pomogaeva

Hydration Energy from a Composite Method for Implicit Representation of Solvent

The CMIRS1.0 (composite method for implicit representation of solvent, Version 1.0) model is introduced for efficacious and inexpensive computation of hydration free energies. The method collects together several disparate models designed to describe short-range dispersion, exchange, and hydrogen bonding interactions as well as long-range electrostatic interactions. All the interactions are formulated as functionals of the solute charge density. The model uses only six adjustable parameters to determine the various short-range terms. In conjunction with an isodensity criterion that uses one parameter to determine the solute cavity size and shape, the model is tested on a large database of neutral and ionic solutes in water. The mean unsigned error compared to experiment is found to be as low as 0.8 kcal/mol for neutral solutes and 2.4 kcal/mol for ionic solutes, which is comparable to or better than other analogous approaches in the literature that invoke many more fitting parameters.

Band structures built by the elongation method

A recently proposed approach for extracting band structures from finite-cluster calculations is improved so that (avoided) band crossings can be handled and the problems related to so-called doublings and holes are reduced. In particular, we demonstrate how the method can be combined with the elongation method for the finite-system calculations and apply it to extracting band structures for polymers from oligomer calculations. As illustrations of the approach we discuss a chain of water molecules, polyacetylene, polyethylene, and a BN nanotube without and with an impurity.

Band structure built from oligomer calculations

A method to build accurate band structures of polymers from oligomer calculations has been developed. This method relies on systematic procedures for (i) assigning k values, (2) eliminating strongly localized molecular orbitals, and (iii) connecting bands across the entire Brillouin zone. Illustrative calculations are carried out at the HF/STO-3G level for trans-polyacetylene (PA), poly(para-phenylene) (PPP), and water chains. More stringent tests at several different levels are reported for polydiacetylene/polybutatriene.

Field-Extremum Model for Short-Range Contributions to Hydration Free Energy

The performance in describing hydration free energies of a broad class of neutral, cationic, and anionic solutes is tested for the recently proposed FESR (Field-Extremum Short-Range) implicit solvation model for interactions between the solute and nearby water molecules, as taken in conjunction with the previously developed SS(V)PE (Surface and Simulation of Volume Polarization for Electrostatics) dielectric continuum model for long-range interactions with bulk water. The empirical FESR model mainly describes solute-water hydrogen bonding interactions by correlating them with the maximum and minimum values of the electric field produced by the solute at the surface of the cavity that excludes solvent. A preliminary report showed that, with only four adjustable parameters, the FESR model, in conjunction with SS(V)PE, can produce hydration energies comparable to the best analogous efforts in the literature that utilized many more parameters. Here, the performance of the FESR model is more fully documented in several respects. The dependence on the underlying quantum mechanical method used to treat the internal electronic structure of the solute is tested by comparing uncorrelated Hartree-Fock to correlated density functional calculations and by comparing a modest sized to a large basis set. The influence of cavity size is studied in connection with an isodensity contour construction of the cavity. The sensitivity of the results to the parameters in the FESR model is considered, and it is found that the dependence on the electric field strength is quite nonlinear, with an optimum exponent consistently in the range of 3 to 4. Overall, it is concluded that the FESR model shows considerable utility for improving the accuracy of implicit models of aqueous solvation.

New implicit solvation models for dispersion and exchange energies.

Implicit solvation models provide a very efficient means to estimate solvation energies. For example, dielectric continuum models are commonly used to obtain the long-range electrostatic interactions. These may be parametrized to also include in some average manner short-range interactions such as dispersion and exchange, but it is preferable to instead develop additional implicit models specifically designed for the short-range interactions. This work proposes new models for dispersion and exchange interactions between solute and solvent by adapting approaches previously developed for treatment of gas-phase intermolecular forces. The new models are formulated in terms of the charge densities of the solutes and use only three adjustable parameters. To illustrate the performance of the models, electronic structure calculations are reported for a large number of solutes in two nonpolar solvents where short-range interactions dominate and different balances pertain between attractive dispersion and repulsive exchange contributions. After empirical optimization of the requisite parameters, it is found that the errors compared to experimental solvation free energies are only about 0.4 kcal/mol on average, which is better than previous approaches in the literature that invoke many more parameters.

Absorption Spectra of Estradiol and Tryptophan Constructed by the Statistical and Elongation Methods

The statistical quantum chemical/molecular dynamical method is developed and employed to reproduce optical spectra. This technique includes quantum-mechanical calculations on energy states and photophysical properties of molecular conformers obtained during molecular dynamical simulation. Polycyclic organic molecule estradiol surrounded by solvent particles and protein structure including tryptophan fragment under thermodynamical conditions are considered. A wide absorption spectrum over several excited electronic states of estradiol is constructed. First longwave absorption band of tryptophan-cage mini protein is built involving the elongation method. These statistical spectra reflect the main features of the corresponding experimental ones.

Composite method for implicit representation of solvent in dimethyl sulfoxide and acetonitrile.

A composite method for implicit representation of solvent previously developed to compute aqueous free energies of solvation is extended to accommodate the polar aprotic solvents dimethyl sulfoxide and acetonitrile. The method combines quantum mechanical calculation of the solute electronic structure with a modern dielectric continuum model for long-range electrostatic interactions with solvent and individual models for short-range interactions arising from dispersion, exchange, and hydrogen bonding. The few parameters involved are optimized to fit a standard data set of experimental solvation energies for neutrals and ions. Results are better than other models in the literature, with average errors for ions comparable to or smaller than the estimated experimental errors. Some circumstantial evidence is also obtained to support one of the competing extrathermodynamic arguments recently used to determine the solvation energies of the proton, which are needed to separate measurements of paired cation plus anion solvation energies into absolute single ion solvation energies in these solvents.

Mechanisms of Hydrogen Generation from Tetrameric Clusters of Lithium Amidoborane.

The first-principles study of dehydrogenation mechanism of tetrameric clusters of lithium amidoborane LiNH2BH3, (LiAB)4, is presented. The choice of tetramer is based on the suspicion that dimeric cluster models used in previous theoretical studies are too small to capture the essence of the reaction. Dehydrogenation pathways starting from three isomers of (LiAB)4 tetramers were explored by applying the artificial force induced reaction (AFIR) method at the M06 level of theory. All obtained reaction pathways feature initial dimerization of two LiAB molecules in the tetramer. Formation of intermediates containing the Li3H moiety is a very characteristic feature of all pathways. In the succeeding rate-limiting step of the release of H2 molecule, a hydridic H atom of the Li3H moiety activates a protic H atom of the NH2 group with formation of the Li2H2 moiety in transition state. The most kinetically favorable pathway has the activation enthalpy of 26.6 kcal mol(-1), substantially lower than that found for dimeric cluster. The obtained results suggest that only three LiAB molecules directly participate in the elementary reactions.

Hydrogen Atom in Water from Ambient to High Temperatures

The aqueous hydrogen atom is studied with molecular dynamics simulations from ambient temperature to near the critical point. The radial distribution functions find a hydrogen atom coordination number of about 13 water molecules at 300 K to about 4 water molecules at 646 K. The radial and angular distribution functions indicate that first-shell water molecules tend to orient to maximize hydrogen bonding interactions with other water molecules. These orientational tendencies diminish with temperature. The calculated diffusion coefficient agrees very well with experimental results known near ambient temperatures. It fits a simple activation model to about 575 K, above which the diffusion becomes much faster than predicted by the fit. To temperatures of at least 500 K there is evidence for caging on a time scale of about 1 ps, but the evidence disappears at very high temperatures. Values of the aqueous hydrogen hyperfine coupling constant are obtained by averaging the results of density functional calculations on clusters extracted from the simulations. The hyperfine coupling calculations do not agree well with experiment for reasons that are not understood now, pointing to the need for further research on this problem.

Efficient algorithm for computing orbital energies within elongation method

We developed a new approach for solving eigenvalue problem for the oligomer chain systems based on localized molecular orbitals (LMO) of the separated fragments within elongation method. The method performed in this work and implemented in elongation scheme yields excellent agreement with the conventional results. It has been demonstrated that the proposed algorithm for computing orbital energies and eigenvectors in elongation method reduces the CPU time usage up to 50%.